public static void checkMetaFile(String file) { if (!isMetaFile(file)) { throw new IllegalArgumentException("Not a valid transformed variants metadata file : " + file); } }
public static String getOriginalFromTransformedFile(String variantsFile) { if (isTransformedVariants(variantsFile)) { int idx = variantsFile.lastIndexOf(VARIANTS_FILE); return variantsFile.substring(0, idx - 1); } else if (isMetaFile(variantsFile)) { int idx = variantsFile.lastIndexOf(METADATA_FILE); return variantsFile.substring(0, idx - 1); } else { return variantsFile; } }
if (isMetaFile(input.toString())) { try (InputStream inputStream = FileUtils.newInputStream(input)) { return VariantReaderUtils.readVariantFileMetadataFromJson(inputStream);
@Test public void validVariantsFile() { assertTrue(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.avro.gz")); assertTrue(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.avro")); assertTrue(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.json")); assertTrue(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.json.gz")); assertTrue(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.proto.gz")); assertTrue(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.proto")); assertFalse(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.gz.txt")); assertFalse(VariantReaderUtils.isTransformedVariants("file.vcf.gz.variants.gz")); assertFalse(VariantReaderUtils.isTransformedVariants("file.vcf")); assertFalse(VariantReaderUtils.isTransformedVariants("s1_variants.genomes.vcf.gz")); assertTrue(VariantReaderUtils.isMetaFile("file.vcf.file.json.gz")); assertFalse(VariantReaderUtils.isMetaFile("file.vcf.file.json")); assertFalse(VariantReaderUtils.isMetaFile("file.vcf.file.avro.gz")); assertFalse(VariantReaderUtils.isMetaFile("file.vcf.file.avro")); assertFalse(VariantReaderUtils.isMetaFile("file.vcf.file.proto")); }